If you're going to think of new weapon ideas, I think the best direction to go isn't in terms of power, but in terms of uniqueness. For example, I'm thinking of having one of my agents use a set of throwing axes. I haven't seen that done before, and it'd be kind of a trademark. (Plus, some of the sue types would really look better with an axe through their foreheads, don'tcha think?)

In terms of weapons, interesting is a hundred times better than powerful. Agents aren't supposed to be particularly powerful, because any kind of power overload puts them in danger of turning into mary sues themselves, which has happened, and which generally ends with the agent in question either having to be assassinated himself, or having to undergo intense treatment to get his non-sue/stu self back. If they do something crazy awesome, it's either because they've botched things badly and had to scramble to survive, or because the sue in question is just that bad and they got cornered. So it's more a question of creativity and caution than guns-blazing overly powerful characters.

They're also not supposed to use weapons that don't fit into the canon they're policing (this is why blades of some sort are popular--they'll fit into just about anything). Using uncanonical weapons tends to defeat the purpose of removing uncanonical things in fics, after all. So your BFG would fit into some video games and a few comic books, but not most other continua.

The point is not to be powerful, but to be interesting. Missions can get repetitive after a while because badfic itself is often quite repetitive; so your agents have to get their own style in order to be interesting.

I definitely think getting creative with weapons would be a great idea; but you'd have to think of which world you're going into, and whether your weapon would fit in; also what your agent's personality is and why s/he favors that weapon. You could use an improvised weapon, for example, like a big heavy cooking pan; or you could have someone use a trademark poison (got to be a canon substance, remember--and research its effects first). Some agents use depowered Sue weapons, often fancy swords with the powers taken out of them to avoid Sue-ifying the agent.

A non-human agent could use physical or mental powers that are natural to him; similarly, an agent in a disguise with various sorts of powers could use those powers (ex. an Uruk-Hai disguise is strong enough to snap a mary-sue's neck, or to handle a longbow that requires a lot of strength to pull). Once again, power levels that are too high are really risky.

Anyway, point being: Be creative, but watch your power levels, or you might find your agents being hauled off for having too high a blood glitter level...

....hammer + Nunchucks? Gitter-draining ball? Spring loaded Sheild? Explosive Slash Harkens? Taser-glove? Or Power Feet to kick Gary Stus in the bishie makers?

Otherwise, I think this is a good idea.